SkillMD SkillMD
light-dark-mode
Profile My skills Saved Collections Edit profile Submit a skill

← all plugins

Scientific Agent Skills

by @k-dense-ai · plugin · 149 skills

Scientific Agent Skills from K-Dense-AI/scientific-agent-skills.

Install the whole plugin (CLI)
npx skillmds add k-dense-ai/esm npx skillmds add k-dense-ai/pdf npx skillmds add k-dense-ai/aeon npx skillmds add k-dense-ai/bids npx skillmds add k-dense-ai/dask npx skillmds add k-dense-ai/cirq npx skillmds add k-dense-ai/gget npx skillmds add k-dense-ai/pptx npx skillmds add k-dense-ai/docx npx skillmds add k-dense-ai/pymc npx skillmds add k-dense-ai/shap npx skillmds add k-dense-ai/vaex npx skillmds add k-dense-ai/xlsx npx skillmds add k-dense-ai/gtars npx skillmds add k-dense-ai/modal npx skillmds add k-dense-ai/pymoo npx skillmds add k-dense-ai/arbor npx skillmds add k-dense-ai/pysam npx skillmds add k-dense-ai/pytdc npx skillmds add k-dense-ai/qutip npx skillmds add k-dense-ai/rdkit npx skillmds add k-dense-ai/rowan npx skillmds add k-dense-ai/simpy npx skillmds add k-dense-ai/depmap npx skillmds add k-dense-ai/flowio npx skillmds add k-dense-ai/geniml npx skillmds add k-dense-ai/pathml npx skillmds add k-dense-ai/sympy npx skillmds add k-dense-ai/polars npx skillmds add k-dense-ai/qiskit npx skillmds add k-dense-ai/scanpy npx skillmds add k-dense-ai/scvelo npx skillmds add k-dense-ai/matlab npx skillmds add k-dense-ai/adaptyv npx skillmds add k-dense-ai/anndata npx skillmds add k-dense-ai/astropy npx skillmds add k-dense-ai/cobrapy npx skillmds add k-dense-ai/datamol npx skillmds add k-dense-ai/lamindb npx skillmds add k-dense-ai/matchms npx skillmds add k-dense-ai/medchem npx skillmds add k-dense-ai/molfeat npx skillmds add k-dense-ai/onekgpd npx skillmds add k-dense-ai/primekg npx skillmds add k-dense-ai/pydicom npx skillmds add k-dense-ai/seaborn npx skillmds add k-dense-ai/arboreto npx skillmds add k-dense-ai/deepchem npx skillmds add k-dense-ai/diffdock npx skillmds add k-dense-ai/fluidsim npx skillmds add k-dense-ai/histolab npx skillmds add k-dense-ai/networkx npx skillmds add k-dense-ai/nextflow npx skillmds add k-dense-ai/pi-agent npx skillmds add k-dense-ai/pydeseq2 npx skillmds add k-dense-ai/pyhealth npx skillmds add k-dense-ai/pymatgen npx skillmds add k-dense-ai/pyopenms npx skillmds add k-dense-ai/pyzotero npx skillmds add k-dense-ai/tamarind npx skillmds add k-dense-ai/autoskill npx skillmds add k-dense-ai/biopython npx skillmds add k-dense-ai/deeptools npx skillmds add k-dense-ai/geomaster npx skillmds add k-dense-ai/geopandas npx skillmds add k-dense-ai/hypogenic npx skillmds add k-dense-ai/liteparse npx skillmds add k-dense-ai/neurokit2 npx skillmds add k-dense-ai/pennylane npx skillmds add k-dense-ai/pufferlib npx skillmds add k-dense-ai/tiledbvcf npx skillmds add k-dense-ai/torchdrug npx skillmds add k-dense-ai/etetoolkit npx skillmds add k-dense-ai/exa-search npx skillmds add k-dense-ai/markitdown npx skillmds add k-dense-ai/matplotlib npx skillmds add k-dense-ai/pacsomatic npx skillmds add k-dense-ai/paperzilla npx skillmds add k-dense-ai/polars-bio npx skillmds add k-dense-ai/pylabrobot npx skillmds add k-dense-ai/scikit-bio npx skillmds add k-dense-ai/scvi-tools npx skillmds add k-dense-ai/umap-learn npx skillmds add k-dense-ai/bioservices npx skillmds add k-dense-ai/bulk-rnaseq npx skillmds add k-dense-ai/peer-review npx skillmds add k-dense-ai/statsmodels npx skillmds add k-dense-ai/zarr-python npx skillmds add k-dense-ai/infographics npx skillmds add k-dense-ai/paper-lookup npx skillmds add k-dense-ai/parallel-web npx skillmds add k-dense-ai/scikit-learn npx skillmds add k-dense-ai/transformers npx skillmds add k-dense-ai/usfiscaldata npx skillmds add k-dense-ai/latex-posters npx skillmds add k-dense-ai/open-notebook npx skillmds add k-dense-ai/phylogenetics npx skillmds add k-dense-ai/pptx-posters npx skillmds add k-dense-ai/dhdna-profiler npx skillmds add k-dense-ai/generate-image npx skillmds add k-dense-ai/what-if-oracle npx skillmds add k-dense-ai/database-lookup npx skillmds add k-dense-ai/hugging-science npx skillmds add k-dense-ai/research-grants npx skillmds add k-dense-ai/research-lookup npx skillmds add k-dense-ai/scikit-survival npx skillmds add k-dense-ai/torch-geometric npx skillmds add k-dense-ai/treatment-plans npx skillmds add k-dense-ai/venue-templates npx skillmds add k-dense-ai/cellxgene-census npx skillmds add k-dense-ai/clinical-reports npx skillmds add k-dense-ai/ginkgo-cloud-lab npx skillmds add k-dense-ai/glycoengineering npx skillmds add k-dense-ai/optimize-for-gpu npx skillmds add k-dense-ai/bgpt-paper-search npx skillmds add k-dense-ai/literature-review npx skillmds add k-dense-ai/omero-integration npx skillmds add k-dense-ai/pytorch-lightning npx skillmds add k-dense-ai/scientific-slides npx skillmds add k-dense-ai/stable-baselines3 npx skillmds add k-dense-ai/statistical-power npx skillmds add k-dense-ai/molecular-dynamics npx skillmds add k-dense-ai/pathway-enrichment npx skillmds add k-dense-ai/scholar-evaluation npx skillmds add k-dense-ai/scientific-writing npx skillmds add k-dense-ai/citation-management npx skillmds add k-dense-ai/experimental-design npx skillmds add k-dense-ai/timesfm-forecasting npx skillmds add k-dense-ai/dnanexus-integration npx skillmds add k-dense-ai/imaging-data-commons npx skillmds add k-dense-ai/latchbio-integration npx skillmds add k-dense-ai/neuropixels-analysis npx skillmds add k-dense-ai/benchling-integration npx skillmds add k-dense-ai/consciousness-council npx skillmds add k-dense-ai/hypothesis-generation npx skillmds add k-dense-ai/opentrons-integration npx skillmds add k-dense-ai/scientific-schematics npx skillmds add k-dense-ai/labarchive-integration npx skillmds add k-dense-ai/get-available-resources npx skillmds add k-dense-ai/statistical-analysis npx skillmds add k-dense-ai/iso-13485-certification npx skillmds add k-dense-ai/market-research-reports npx skillmds add k-dense-ai/protocolsio-integration npx skillmds add k-dense-ai/markdown-mermaid-writing npx skillmds add k-dense-ai/scientific-brainstorming npx skillmds add k-dense-ai/scientific-visualization npx skillmds add k-dense-ai/clinical-decision-support npx skillmds add k-dense-ai/exploratory-data-analysis npx skillmds add k-dense-ai/scientific-critical-thinking
⬇ Download

Skills in this plugin

  1. ▌
    esm · k-dense-ai bundle
    Generate, predict, and embed protein sequences and structures using ESM3, ESMC, and ESMFold2 with local or cloud inference.
    30.2k
    repo stars
  2. ▌
    pdf · k-dense-ai bundle
    Read, extract, merge, split, rotate, watermark, encrypt, and OCR PDF files using Python libraries and command-line tools.
    30.2k
    repo stars
  3. ▌
    aeon · k-dense-ai bundle
    Perform time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search using a scikit-learn compatible Python toolkit.
    30.2k
    repo stars
  4. ▌
    bids · k-dense-ai bundle
    Organize, query, validate, and convert neuroscience and biomedical data using the Brain Imaging Data Structure (BIDS) standard.
    30.2k
    repo stars
  5. ▌
    dask · k-dense-ai bundle
    Scale pandas and NumPy workflows to larger-than-memory datasets using parallel and distributed computing.
    30.2k
    repo stars
  6. ▌
    cirq · k-dense-ai bundle
    Design, simulate, and run quantum circuits on Google Quantum AI hardware and partner backends using Cirq.
    30.2k
    repo stars
  7. ▌
    gget · k-dense-ai bundle
    Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.
    30.2k
    repo stars
  8. ▌
    pptx · k-dense-ai bundle
    Create, read, edit, and convert .pptx presentations with design guidance, template manipulation, and visual QA workflows.
    30.2k
    repo stars
  9. ▌
    docx · k-dense-ai bundle
    Create, read, edit, and manipulate Word documents (.docx) with formatting, tables, images, and tracked changes.
    30.2k
    repo stars
  10. ▌
    pymc · k-dense-ai bundle
    Build, fit, validate, and compare Bayesian models using PyMC's modern API, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.
    30.2k
    repo stars
  11. ▌
    shap · k-dense-ai bundle
    Explain machine learning model predictions using SHAP values, compute feature importance, and generate visualizations including waterfall, beeswarm, bar, scatter, force, and heatmap plots.
    30.2k
    repo stars
  12. ▌
    vaex · k-dense-ai bundle
    Process and analyze large tabular datasets (billions of rows) that exceed available RAM using lazy, out-of-core DataFrames with fast aggregations, visualization, and machine learning integration.
    30.2k
    repo stars
  13. ▌
    xlsx · k-dense-ai bundle
    Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) with formulas, formatting, financial models, and multi-sheet workbooks.
    30.2k
    repo stars
  14. ▌
    gtars · k-dense-ai bundle
    High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
    30.2k
    repo stars
  15. ▌
    modal · k-dense-ai bundle
    Deploy and serve AI/ML models on Modal's serverless cloud platform with on-demand GPUs, autoscaling containers, persistent storage, and scheduled jobs.
    30.2k
    repo stars
  16. ▌
    pymoo · k-dense-ai bundle
    Solve single and multi-objective optimization problems using NSGA-II/III, MOEA/D, and other evolutionary algorithms with customizable operators, constraint handling, and benchmark problems.
    30.2k
    repo stars
  17. ▌
    arbor · k-dense-ai bundle
    Run autonomous optimization loops that iteratively improve artifacts against evaluators using hypothesis tree refinement, without overfitting.
    30.2k
    repo stars
  18. ▌
    pysam · k-dense-ai bundle
    Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.
    30.2k
    repo stars
  19. ▌
    pytdc · k-dense-ai bundle
    Access AI-ready drug discovery datasets and benchmarks from Therapeutics Data Commons, covering ADME, toxicity, drug-target interactions, and molecular generation with standardized splits and evaluation metrics.
    30.2k
    repo stars
  20. ▌
    qutip · k-dense-ai bundle
    Simulate and analyze open quantum systems using QuTiP, including master equations, Lindblad dynamics, decoherence, and quantum optics.
    30.2k
    repo stars
  21. ▌
    rdkit · k-dense-ai bundle
    Perform cheminformatics tasks including molecular I/O, descriptor calculation, fingerprinting, substructure search, and similarity analysis using the RDKit library.
    30.2k
    repo stars
  22. ▌
    rowan · k-dense-ai
    Run cloud-native molecular modeling and drug-design workflows including pKa prediction, docking, molecular dynamics, and protein-ligand cofolding via a Python API.
    30.2k
    repo stars
  23. ▌
    simpy · k-dense-ai bundle
    Build discrete-event simulations of systems with processes, queues, resources, and time-based events using SimPy in Python.
    30.2k
    repo stars
  24. ▌
    depmap · k-dense-ai bundle
    Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.
    30.2k
    repo stars
  25. ▌
    flowio · k-dense-ai bundle
    Parse FCS (Flow Cytometry Standard) files v2.0-3.1, extract events as NumPy arrays, read metadata and channels, and convert to CSV or DataFrame for flow cytometry data preprocessing.
    30.2k
    repo stars
  26. ▌
    geniml · k-dense-ai bundle
    Train unsupervised machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.
    30.2k
    repo stars
  27. ▌
    pathml · k-dense-ai bundle
    Analyze whole-slide pathology images with Python: load 160+ slide formats, preprocess H&E stains, segment nuclei, construct spatial graphs, train ML models, and process multiplex immunofluorescence data (CODEX, Vectra).
    30.2k
    repo stars
  28. ▌
    sympy · k-dense-ai bundle
    Perform exact symbolic mathematics in Python — algebra, calculus, equation solving, symbolic linear algebra, and code generation via lambdify or LaTeX.
    30.2k
    repo stars
  29. ▌
    polars · k-dense-ai bundle
    Process data with high-performance DataFrames using Polars' expression-based API, lazy evaluation, and parallel execution for ETL, analytics, and pandas migration.
    30.2k
    repo stars
  30. ▌
    qiskit · k-dense-ai bundle
    Build and execute quantum circuits on IBM Quantum hardware, simulators, and third-party providers using the Qiskit framework.
    30.2k
    repo stars
  31. ▌
    scanpy · k-dense-ai bundle
    Run standard single-cell RNA-seq analysis pipelines: QC, normalization, dimensionality reduction, clustering, differential expression, and visualization using Scanpy.
    30.2k
    repo stars
  32. ▌
    scvelo · k-dense-ai bundle
    Estimate cell state transitions from unspliced/spliced mRNA dynamics using scVelo, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data.
    30.2k
    repo stars
  33. ▌
    matlab · k-dense-ai bundle
    Perform numerical computing, matrix operations, data analysis, and scientific visualization using MATLAB or GNU Octave.
    30.2k
    repo stars
  34. ▌
    adaptyv · k-dense-ai bundle
    Submit protein sequences to the Adaptyv Bio Foundry for experimental characterization (binding, thermostability, expression, fluorescence) and retrieve results via API or Python SDK.
    30.2k
    repo stars
  35. ▌
    anndata · k-dense-ai bundle
    Create, read, manipulate, and store annotated data matrices using the AnnData Python package, designed for single-cell genomics and general-purpose annotated data workflows.
    30.2k
    repo stars
  36. ▌
    astropy · k-dense-ai bundle
    Perform astronomical data analysis with Astropy: coordinate transformations, unit conversions, FITS I/O, cosmological calculations, time handling, table operations, and WCS transformations.
    30.2k
    repo stars
  37. ▌
    cobrapy · k-dense-ai bundle
    Perform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.
    30.2k
    repo stars
  38. ▌
    datamol · k-dense-ai bundle
    Simplify molecular cheminformatics with a Pythonic wrapper around RDKit for SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel processing.
    30.2k
    repo stars
  39. ▌
    lamindb · k-dense-ai bundle
    Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.
    30.2k
    repo stars
  40. ▌
    matchms · k-dense-ai bundle
    Process and analyze mass spectrometry data: import spectra from MGF, mzML, MSP, and JSON formats; apply 40+ filters for metadata harmonization and peak cleaning; compute spectral similarities (cosine, modified cosine) for compound identification; build reproducible processing pipelines.
    30.2k
    repo stars
  41. ▌
    medchem · k-dense-ai bundle
    Apply medicinal chemistry filters for compound triage: drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and a custom query language for library filtering.
    30.2k
    repo stars
  42. ▌
    molfeat · k-dense-ai bundle
    Convert chemical structures (SMILES or RDKit molecules) into numerical representations for machine learning using 100+ featurizers, including ECFP, MACCS, descriptors, and pretrained models like ChemBERTa.
    30.2k
    repo stars
  43. ▌
    onekgpd · k-dense-ai bundle
    Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.
    30.2k
    repo stars
  44. ▌
    primekg · k-dense-ai bundle
    Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
    30.2k
    repo stars
  45. ▌
    pydicom · k-dense-ai bundle
    Read, write, and modify DICOM medical imaging files, including pixel data extraction, metadata manipulation, anonymization, and format conversion.
    30.2k
    repo stars
  46. ▌
    seaborn · k-dense-ai bundle
    Create publication-quality statistical graphics with dataset-oriented plotting, multivariate analysis, and automatic statistical estimation using minimal code.
    30.2k
    repo stars
  47. ▌
    arboreto · k-dense-ai bundle
    Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.
    30.2k
    repo stars
  48. ▌
    deepchem · k-dense-ai bundle
    Predict molecular properties, train graph neural networks, and run drug discovery workflows using DeepChem's featurizers, models, and MoleculeNet benchmarks.
    30.2k
    repo stars
  49. ▌
    diffdock · k-dense-ai bundle
    Predict 3D binding poses of small molecule ligands to protein targets using diffusion-based molecular docking, supporting single complexes, batch processing, and virtual screening.
    30.2k
    repo stars
  50. ▌
    fluidsim · k-dense-ai bundle
    Run computational fluid dynamics simulations using Python, including Navier-Stokes equations, shallow water, and stratified flows with pseudospectral methods and HPC support.
    30.2k
    repo stars
  51. ▌
    histolab · k-dense-ai bundle
    Process whole slide images for digital pathology: detect tissue, extract tiles, and prepare datasets for deep learning pipelines.
    30.2k
    repo stars
  52. ▌
    networkx · k-dense-ai bundle
    Create, analyze, and visualize complex networks and graphs in Python with NetworkX, including graph algorithms, community detection, synthetic network generation, and multiple I/O formats.
    30.2k
    repo stars
  53. ▌
    nextflow · k-dense-ai bundle
    Build, run, and debug Nextflow data pipelines and nf-core workflows end to end, covering processes, channels, operators, configuration, testing, and deployment to HPC or cloud.
    30.2k
    repo stars
  54. ▌
    pi-agent · k-dense-ai bundle
    Install, configure, and extend Pi, a terminal coding harness, with support for custom providers, models, extensions, skills, packages, themes, SDK integration, RPC mode, JSON event streams, and ecosystem packages for subagent delegation, MCP servers, interactive forms, and web access.
    30.2k
    repo stars
  55. ▌
    pydeseq2 · k-dense-ai bundle
    Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
    30.2k
    repo stars
  56. ▌
    pyhealth · k-dense-ai bundle
    Build clinical deep-learning pipelines with PyHealth: load EHR, signal, and imaging datasets, define prediction tasks, instantiate models, train with the PyHealth Trainer, and compute clinical metrics.
    30.2k
    repo stars
  57. ▌
    pymatgen · k-dense-ai bundle
    Analyze and manipulate crystal structures, compute phase diagrams, and access the Materials Project database using the pymatgen library.
    30.2k
    repo stars
  58. ▌
    pyopenms · k-dense-ai bundle
    Analyze proteomics and metabolomics mass spectrometry data with PyOpenMS: read/write MS file formats, process spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines using ready-to-run scripts.
    30.2k
    repo stars
  59. ▌
    pyzotero · k-dense-ai bundle
    Manage Zotero reference libraries programmatically using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3.
    30.2k
    repo stars
  60. ▌
    tamarind · k-dense-ai bundle
    Run computational biology tools for protein structure prediction, design, docking, and molecular dynamics on managed cloud GPUs via REST API or MCP server.
    30.2k
    repo stars
  61. ▌
    autoskill · k-dense-ai bundle
    Analyze recent screen activity via a local screenpipe daemon, detect repeated research workflows, and draft new skills or composition recipes for uncovered patterns.
    30.2k
    repo stars
  62. ▌
    biopython · k-dense-ai bundle
    Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.
    30.2k
    repo stars
  63. ▌
    deeptools · k-dense-ai bundle
    Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.
    30.2k
    repo stars
  64. ▌
    geomaster · k-dense-ai bundle
    Process satellite imagery, perform GIS analysis, and apply spatial machine learning across 70+ geospatial topics with code examples in 8 programming languages.
    30.2k
    repo stars
  65. ▌
    geopandas · k-dense-ai bundle
    Extends pandas for geospatial vector data analysis, including reading/writing shapefiles, GeoJSON, GeoPackage, and PostGIS, performing spatial joins, geometric operations, coordinate transformations, and creating static or interactive maps.
    30.2k
    repo stars
  66. ▌
    hypogenic · k-dense-ai bundle
    Automates hypothesis generation and testing on tabular datasets using LLMs, combining data-driven discovery with literature integration for scientific research.
    30.2k
    repo stars
  67. ▌
    liteparse · k-dense-ai bundle
    Parse PDFs, Office files, and images locally with layout-preserved text, bounding boxes, OCR, and page screenshots for RAG and multimodal agents.
    30.2k
    repo stars
  68. ▌
    neurokit2 · k-dense-ai bundle
    Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.
    30.2k
    repo stars
  69. ▌
    pennylane · k-dense-ai bundle
    Train quantum circuits like neural networks with automatic differentiation, device-independent programming, and integration with PyTorch or JAX.
    30.2k
    repo stars
  70. ▌
    pufferlib · k-dense-ai bundle
    Train reinforcement learning agents at millions of steps per second using optimized PPO, vectorized environments, and multi-agent support.
    30.2k
    repo stars
  71. ▌
    tiledbvcf · k-dense-ai
    Store, query, and export genomic variant data (VCF/BCF) using TileDB's sparse array technology for scalable population genomics workflows.
    30.2k
    repo stars
  72. ▌
    torchdrug · k-dense-ai bundle
    Build and train graph neural networks for drug discovery, protein modeling, and molecular science using PyTorch-native tools.
    30.2k
    repo stars
  73. ▌
    etetoolkit · k-dense-ai bundle
    Manipulate phylogenetic trees, detect evolutionary events, integrate NCBI taxonomy, and create publication-quality visualizations using the ETE toolkit.
    30.2k
    repo stars
  74. ▌
    exa-search · k-dense-ai bundle
    Search the web and extract content from URLs using Exa, with support for academic and scientific sources.
    30.2k
    repo stars
  75. ▌
    markitdown · k-dense-ai bundle
    Convert files and office documents to Markdown using Microsoft's MarkItDown tool. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
    30.2k
    repo stars
  76. ▌
    matplotlib · k-dense-ai bundle
    Create publication-quality static, animated, and interactive plots with fine-grained control over every element using Matplotlib's pyplot and object-oriented APIs.
    30.2k
    repo stars
  77. ▌
    pacsomatic · k-dense-ai bundle
    Validates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).
    30.2k
    repo stars
  78. ▌
    paperzilla · k-dense-ai
    Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Fetch feeds, read papers, leave feedback, and export data using the pz CLI.
    30.2k
    repo stars
  79. ▌
    polars-bio · k-dense-ai bundle
    Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.
    30.2k
    repo stars
  80. ▌
    pylabrobot · k-dense-ai bundle
    Control liquid handling robots, plate readers, pumps, and other lab equipment through a unified Python interface across platforms.
    30.2k
    repo stars
  81. ▌
    scikit-bio · k-dense-ai bundle
    Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.
    30.2k
    repo stars
  82. ▌
    scvi-tools · k-dense-ai bundle
    Provides deep generative models for single-cell omics analysis, including probabilistic batch correction, transfer learning, differential expression, and multi-modal integration.
    30.2k
    repo stars
  83. ▌
    umap-learn · k-dense-ai bundle
    Perform nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows using the umap-learn library.
    30.2k
    repo stars
  84. ▌
    bioservices · k-dense-ai bundle
    Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.
    30.2k
    repo stars
  85. ▌
    bulk-rnaseq · k-dense-ai bundle
    Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.
    30.2k
    repo stars
  86. ▌
    peer-review · k-dense-ai bundle
    Evaluate scientific manuscripts and grant proposals with structured, checklist-based peer review covering methodology, statistics, reproducibility, ethics, and reporting standards.
    30.2k
    repo stars
  87. ▌
    statsmodels · k-dense-ai bundle
    Fit statistical models (OLS, GLM, ARIMA, mixed models) with detailed diagnostics, residuals, and inference for econometrics and time series analysis.
    30.2k
    repo stars
  88. ▌
    zarr-python · k-dense-ai bundle
    Store and process large N-dimensional arrays with chunking, compression, and parallel I/O, integrating with NumPy, Dask, and Xarray for cloud-native scientific computing.
    30.2k
    repo stars
  89. ▌
    infographics · k-dense-ai bundle
    Generate publication-quality infographics using Nano Banana Pro AI with Gemini 3 Pro quality review and optional Perplexity Sonar research. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.
    30.2k
    repo stars
  90. ▌
    paper-lookup · k-dense-ai bundle
    Search 10 academic literature APIs for papers, preprints, citations, and open-access full text with reproducible provenance.
    30.2k
    repo stars
  91. ▌
    parallel-web · k-dense-ai bundle
    Search the web, extract URL content, enrich datasets with web-sourced fields, and run deep research reports, prioritizing academic and scientific sources.
    30.2k
    repo stars
  92. ▌
    scikit-learn · k-dense-ai bundle
    Build and evaluate machine learning models using scikit-learn for classification, regression, clustering, dimensionality reduction, and preprocessing.
    30.2k
    repo stars
  93. ▌
    transformers · k-dense-ai bundle
    Load pre-trained models from Hugging Face Hub, run pipeline inference, generate text, and fine-tune models on NLP, vision, audio, and multimodal tasks using the Transformers library.
    30.2k
    repo stars
  94. ▌
    usfiscaldata · k-dense-ai bundle
    Query the U.S. Treasury Fiscal Data REST API for federal financial data including national debt, daily and monthly treasury statements, securities auctions, interest rates, exchange rates, savings bonds, and government revenue and spending statistics. No API key required.
    30.2k
    repo stars
  95. ▌
    latex-posters · k-dense-ai bundle
    Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter with layout design, color schemes, multi-column formats, and figure integration.
    30.2k
    repo stars
  96. ▌
    open-notebook · k-dense-ai bundle
    Self-host an open-source research notebook with AI-powered note generation, multi-speaker podcast creation, and context-aware document chat, supporting 16+ AI providers.
    30.2k
    repo stars
  97. ▌
    phylogenetics · k-dense-ai bundle
    Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.
    30.2k
    repo stars
  98. ▌
    pptx-posters · k-dense-ai bundle
    Create research posters using HTML/CSS that can be exported to PDF or PPTX, with AI-generated visual elements and responsive layouts.
    30.2k
    repo stars
  99. ▌
    dhdna-profiler · k-dense-ai bundle
    Analyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.
    30.2k
    repo stars
  100. ▌
    generate-image · k-dense-ai bundle
    Generate and edit high-quality images using OpenRouter's AI models including FLUX.2 Pro and Gemini 3.1 Flash Image Preview.
    30.2k
    repo stars
  101. ▌
    what-if-oracle · k-dense-ai bundle
    Run structured What-If scenario analysis with 4-6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use for speculative questions about uncertain futures, strategic forks, contingency planning, or stress-testing decisions.
    30.2k
    repo stars
  102. ▌
    database-lookup · k-dense-ai bundle
    Query documented public database APIs with explicit endpoints, filters, pagination, and provenance for reproducible retrieval of scientific, regulatory, or financial facts.
    30.2k
    repo stars
  103. ▌
    hugging-science · k-dense-ai bundle
    Discovers and uses scientific datasets, models, blog posts, and interactive demos from a curated catalog for AI/ML work in domains like biology, chemistry, physics, and genomics.
    30.2k
    repo stars
  104. ▌
    research-grants · k-dense-ai bundle
    Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC with agency-specific formatting, review criteria, budget preparation, and compliance guidance.
    30.2k
    repo stars
  105. ▌
    research-lookup · k-dense-ai bundle
    Look up current research and scientific information across three backends: fast web search, deep multi-source synthesis, and scholarly paper searches. Automatically routes each query to the best backend and saves every result for reproducible citation.
    30.2k
    repo stars
  106. ▌
    scikit-survival · k-dense-ai bundle
    Perform survival analysis and time-to-event modeling in Python using scikit-survival, including Cox models, random survival forests, gradient boosting, survival SVMs, and evaluation metrics like concordance index and Brier score.
    30.2k
    repo stars
  107. ▌
    torch-geometric · k-dense-ai bundle
    Build and train graph neural networks with PyTorch Geometric, covering node/link/graph classification, message passing layers, heterogeneous graphs, and custom datasets.
    30.2k
    repo stars
  108. ▌
    treatment-plans · k-dense-ai bundle
    Generate concise (3-4 page) medical treatment plans in LaTeX/PDF format across all clinical specialties, with SMART goals, evidence-based interventions, and HIPAA compliance.
    30.2k
    repo stars
  109. ▌
    venue-templates · k-dense-ai bundle
    Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues, academic conferences, research posters, and grant proposals.
    30.2k
    repo stars
  110. ▌
    cellxgene-census · k-dense-ai bundle
    Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.
    30.2k
    repo stars
  111. ▌
    clinical-reports · k-dense-ai bundle
    Generate comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports, clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries) with templates, regulatory compliance, and validation tools.
    30.2k
    repo stars
  112. ▌
    ginkgo-cloud-lab · k-dense-ai bundle
    Submit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution, including protein expression, purification, quantification, RNA synthesis, and custom workflows via EstiMate.
    30.2k
    repo stars
  113. ▌
    glycoengineering · k-dense-ai bundle
    Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.
    30.2k
    repo stars
  114. ▌
    optimize-for-gpu · k-dense-ai bundle
    GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, and other RAPIDS libraries for dramatic speedups on numerical, data, ML, graph, and simulation workloads.
    30.2k
    repo stars
  115. ▌
    bgpt-paper-search · k-dense-ai
    Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions.
    30.2k
    repo stars
  116. ▌
    literature-review · k-dense-ai bundle
    Conduct systematic literature reviews by searching multiple academic databases, synthesizing findings, and generating professionally formatted documents with verified citations.
    30.2k
    repo stars
  117. ▌
    omero-integration · k-dense-ai bundle
    Access microscopy images and metadata via the OMERO Python API: retrieve datasets, analyze pixels, manage ROIs and annotations, and batch-process for high-content screening workflows.
    30.2k
    repo stars
  118. ▌
    pytorch-lightning · k-dense-ai bundle
    Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), and distributed training (DDP, FSDP, DeepSpeed) for scalable neural network training.
    30.2k
    repo stars
  119. ▌
    scientific-slides · k-dense-ai bundle
    Build visually engaging scientific slide decks for conferences, seminars, defenses, and research talks with structured planning, design templates, and automated image generation.
    30.2k
    repo stars
  120. ▌
    stable-baselines3 · k-dense-ai bundle
    Train reinforcement learning agents using PPO, SAC, DQN, TD3, DDPG, and A2C algorithms with a scikit-learn-like API. Supports custom Gymnasium environments, vectorized environments, callbacks, and model persistence.
    30.2k
    repo stars
  121. ▌
    statistical-power · k-dense-ai bundle
    Calculate sample sizes, minimum detectable effects, and power curves for study planning using closed-form formulas or Monte Carlo simulation.
    30.2k
    repo stars
  122. ▌
    molecular-dynamics · k-dense-ai bundle
    Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).
    30.2k
    repo stars
  123. ▌
    pathway-enrichment · k-dense-ai bundle
    Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.
    30.2k
    repo stars
  124. ▌
    scholar-evaluation · k-dense-ai bundle
    Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
    30.2k
    repo stars
  125. ▌
    scientific-writing · k-dense-ai bundle
    Write scientific manuscripts in full paragraphs using IMRAD structure, with citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA) for research papers and journal submissions.
    30.2k
    repo stars
  126. ▌
    citation-management · k-dense-ai bundle
    Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries.
    30.2k
    repo stars
  127. ▌
    experimental-design · k-dense-ai bundle
    Design experiments and studies before data collection — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable.
    30.2k
    repo stars
  128. ▌
    timesfm-forecasting · k-dense-ai bundle
    Forecast any univariate time series (sales, sensors, energy, vitals, weather) zero-shot using Google's TimesFM foundation model, with point forecasts and prediction intervals from CSV, DataFrame, or array inputs.
    30.2k
    repo stars
  129. ▌
    dnanexus-integration · k-dense-ai bundle
    Build and deploy apps/applets on the DNAnexus cloud genomics platform, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
    30.2k
    repo stars
  130. ▌
    imaging-data-commons · k-dense-ai bundle
    Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
    30.2k
    repo stars
  131. ▌
    latchbio-integration · k-dense-ai bundle
    Build and deploy bioinformatics workflows as serverless pipelines on the Latch platform using Python decorators, cloud data management, and GPU support.
    30.2k
    repo stars
  132. ▌
    neuropixels-analysis · k-dense-ai bundle
    Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface, covering loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.
    30.2k
    repo stars
  133. ▌
    benchling-integration · k-dense-ai bundle
    Integrate with Benchling's Python SDK and REST API to manage registry entities, inventory, ELN entries, workflows, and Data Warehouse queries for life sciences R&D automation.
    30.2k
    repo stars
  134. ▌
    consciousness-council · k-dense-ai bundle
    Simulates a multi-perspective deliberation council to explore complex questions, decisions, or creative challenges from diverse thinking archetypes.
    30.2k
    repo stars
  135. ▌
    hypothesis-generation · k-dense-ai bundle
    Formulate testable hypotheses from observations, design experiments, and generate predictions using a structured scientific method framework.
    30.2k
    repo stars
  136. ▌
    opentrons-integration · k-dense-ai bundle
    Write Opentrons Protocol API v2 protocols for Flex and OT-2 robots to automate liquid handling, control hardware modules, and manage labware configurations.
    30.2k
    repo stars
  137. ▌
    scientific-schematics · k-dense-ai bundle
    Create publication-quality scientific diagrams using AI generation with smart iterative refinement and quality review.
    30.2k
    repo stars
  138. ▌
    labarchive-integration · k-dense-ai bundle
    Access and manage LabArchives electronic lab notebooks programmatically via REST API. Create entries, upload attachments, backup notebooks, generate reports, and integrate with Protocols.io, Jupyter, REDCap, and other scientific tools.
    30.2k
    repo stars
  139. ▌
    get-available-resources · k-dense-ai bundle
    Detects available CPU, GPU, memory, and disk resources and generates strategic recommendations for scientific computing tasks.
    30.2k
    repo stars
  140. ▌
    statistical-analysis · k-dense-ai bundle
    Guides statistical hypothesis testing with assumption checks, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting for research data.
    30.2k
    repo stars
  141. ▌
    iso-13485-certification · k-dense-ai bundle
    Prepare ISO 13485:2016 certification documentation for medical device Quality Management Systems, including gap analysis, template-based document creation, and compliance checklists.
    30.2k
    repo stars
  142. ▌
    market-research-reports · k-dense-ai bundle
    Generate comprehensive, professional-grade market research reports (50+ pages) with LaTeX formatting, strategic frameworks, and data-driven visualizations.
    30.2k
    repo stars
  143. ▌
    protocolsio-integration · k-dense-ai bundle
    Integrates with the protocols.io API v3 to search, create, update, and publish scientific protocols, manage steps and materials, handle discussions, organize workspaces, and upload files.
    30.2k
    repo stars
  144. ▌
    markdown-mermaid-writing · k-dense-ai bundle
    Creates scientific documentation using markdown with embedded Mermaid diagrams as the default format, enforcing a text-based diagram standard with style guides, 24 diagram type references, and document templates.
    30.2k
    repo stars
  145. ▌
    scientific-brainstorming · k-dense-ai bundle
    Generate novel research ideas through structured, conversational brainstorming that explores interdisciplinary connections, challenges assumptions, and identifies research gaps.
    30.2k
    repo stars
  146. ▌
    scientific-visualization · k-dense-ai bundle
    Create publication-ready scientific figures with multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and journal-specific formatting using matplotlib, seaborn, and plotly.
    30.2k
    repo stars
  147. ▌
    clinical-decision-support · k-dense-ai bundle
    Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.
    30.2k
    repo stars
  148. ▌
    exploratory-data-analysis · k-dense-ai bundle
    Automatically detect and analyze scientific data files across 200+ formats, generating detailed markdown reports with quality metrics and analysis recommendations.
    30.2k
    repo stars
  149. ▌
    scientific-critical-thinking · k-dense-ai bundle
    Evaluate scientific claims and evidence quality by assessing experimental design, identifying biases and confounders, and applying evidence grading frameworks like GRADE and Cochrane Risk of Bias.
    30.2k
    repo stars